query regarding error in installation of "goseq" R bioconductor package
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abhisek001 • 0
@6d5973d2
Last seen 3 months ago
India

I am trying to install "goseq" Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are the following please help me.

* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.15.1" && make -f "Makefile.Rhtslib"
make[1]: Entering directory '/tmp/RtmplGFsh2/R.INSTALL33a74238d50d/Rhtslib/src/htslib-1.15.1'
gcc -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -I.  -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -I.  -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -I.  -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -I.  -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -I.  -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -I.  -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -I.  -D_FILE_OFFSET_BITS=64 -c -o header.o header.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -I.  -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h
echo '#define HTS_CC "gcc"' > config_vars.h
echo '#define HTS_CPPFLAGS " -D_FILE_OFFSET_BITS=64"' >> config_vars.h
echo '#define HTS_CFLAGS "-g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-Wl,-Bsymbolic-functions -Wl,-z,relro -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl"' >> config_vars.h
gcc -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -I.  -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
hts.c:46:10: fatal error: lzma.h: No such file or directory
   46 | #include <lzma.h>
      |          ^~~~~~~~
compilation terminated.
make[1]: *** [Makefile.Rhtslib:135: hts.o] Error 1
make[1]: Leaving directory '/tmp/RtmplGFsh2/R.INSTALL33a74238d50d/Rhtslib/src/htslib-1.15.1'
make: *** [Makevars.common:22: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/Rhtslib’
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/GenomicAlignments’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/rtracklayer’
ERROR: dependency ‘rtracklayer’ is not available for package ‘GenomicFeatures’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/GenomicFeatures’
ERROR: dependencies ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘geneLenDataBase’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/geneLenDataBase’
ERROR: dependency ‘geneLenDataBase’ is not available for package ‘goseq’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/goseq’

The downloaded source packages are in
    ‘/tmp/RtmpDANqzq/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, foreign, MASS, Matrix, spatial
Old packages: 'jpeg'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://cloud.r-project.org/src/contrib/jpeg_0.1-10.tar.gz'
Content type 'application/x-gzip' length 18667 bytes (18 KB)
==================================================
downloaded 18 KB

* installing *source* package ‘jpeg’ ...
** package ‘jpeg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c read.c -o read.o
In file included from read.c:1:
rjcommon.h:11:10: fatal error: jpeglib.h: No such file or directory
   11 | #include <jpeglib.h>
      |          ^~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:169: read.o] Error 1
ERROR: compilation failed for package ‘jpeg’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/jpeg’
* restoring previous ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/jpeg’

The downloaded source packages are in
    ‘/tmp/RtmpDANqzq/downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘Rhtslib’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘Rsamtools’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘geneLenDataBase’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘goseq’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘jpeg’ had non-zero exit status
>
R Bioconductor Install • 1.4k views
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It looks like you are missing a system dependency for jpeg. I know on linux you would do something like sudo apt-get install libjpeg-dev. I don't have a mac but I think its something like brew install jpeg and not sure of windows.

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I thank you for your help libjpeg-dev package is now got installed in my ubuntu system but the problem still persists.

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0
Entering edit mode

Is there a different message ?

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0
Entering edit mode

no, those previous errors are still there.

hts.c:46:10: fatal error: lzma.h: No such file or directory
   46 | #include <lzma.h>
      |          ^~~~~~~~
compilation terminated.
make[1]: Leaving directory '/tmp/Rtmp3JV7Sn/R.INSTALL4ffa547efc7a/Rhtslib/src/htslib-1.15.1'
make[1]: *** [Makefile.Rhtslib:135: hts.o] Error 1
make: *** [Makevars.common:22: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/Rhtslib’
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/GenomicAlignments’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/rtracklayer’
ERROR: dependency ‘rtracklayer’ is not available for package ‘GenomicFeatures’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/GenomicFeatures’
ERROR: dependencies ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘geneLenDataBase’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/geneLenDataBase’
ERROR: dependency ‘geneLenDataBase’ is not available for package ‘goseq’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/goseq’

The downloaded source packages are in
    ‘/tmp/RtmpDANqzq/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, foreign, MASS, Matrix, spatial
Old packages: 'jpeg'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://cloud.r-project.org/src/contrib/jpeg_0.1-10.tar.gz'
Content type 'application/x-gzip' length 18667 bytes (18 KB)
==================================================
downloaded 18 KB

* installing *source* package ‘jpeg’ ...
** package ‘jpeg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c read.c -o read.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c reg.c -o reg.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c write.c -o write.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o jpeg.so read.o reg.o write.o -ljpeg -L/usr/lib/R/lib -lR
installing to /home/omic/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-jpeg/00new/jpeg/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (jpeg)

The downloaded source packages are in
    ‘/tmp/RtmpDANqzq/downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘Rhtslib’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘Rsamtools’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘geneLenDataBase’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘goseq’ had non-zero exit status
ADD REPLY •
1
Entering edit mode

searching could be helpful --- lzma.h: No such file or directory means you are missing another system dependency that needs to be installed. apt-get install liblzma-dev

ADD REPLY •
0
Entering edit mode

Thank you so much for showing me to look the pattern of the problem. I think now the package got installed.

ADD REPLY •
0
Entering edit mode

No worries. If a different ERROR occurs please post the output here for further assistance.

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